[svtoolkit-help] PlotGenotyping and tigra_sv

[Ankita i. <an...@ig...>]

Hi Bob,

I have few more issues, i am trying to use plotgenotyping module using
command as follows
command -
java -cp
/data1/home/ankita/1000G_Data/svtoolkit/lib/SVToolkit.jar:/data1/home/1000G_Data/svtoolkit/lib/gatk/GenomeAnalysisTK.jar
 org.broadinstitute.sv.apps.PlotGenotypingResults  -site DEL_147 -o
test.pdf -rundirectory .

Error - Exception in thread "main" java.lang.NoClassDefFoundError:
org/broadinstitute/sv/apps/PlotGenotypingResults
Caused by: java.lang.ClassNotFoundException:
org.broadinstitute.sv.apps.PlotGenotypingResults
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:319)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:264)
at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:332)

I tried to find, but couldn't find the answer.

(ii) for tigra_sv installation - i got cmake file, main.cpp samtools.h file
for installation but unable to install it, Can you guide ?

(iii) While using alt_alignment, we have to  provide unmapped bam
files separately or tool can identify the flags for unmapped reads in a bam
file (supposed downloaded from 1000 Genomes), how to use tigra_sv in
alt_alignment steps, as output of tigra_sv is a text file of breakpoints.

-- 
------------
Regards
Ankita
DST Inspire Fellow (Graduate Student)
Lab no 604A
G.N. Ramachandran Knowledge Center for Genome Informatics
Institute of Genomics and Integrative Biology (CSIR)
North Campus DU, Near Jubliee Hall
Delhi - 110007


http://igvbrowser.igib.res.in